Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008560.1 Hibiscus syriacus cultivar Beakdansim tig00111467_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 753118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:341648 original size:21 final size:21
Alignment explanation
Indices: 341575--341650 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 21
341565 TATCTGAGTA
341575 AATGCATATGTCTAATTGTCG
1 AATGCATATGTCTAATTGTCG
* *
341596 AATGCATCTTTATGTGTGAACTATGT-A
1 AATGCA----TATGTCT-AA-T-TGTCG
341623 AATGCATATGTCTAATTGTCG
1 AATGCATATGTCTAATTGTCG
341644 AATGCAT
1 AATGCAT
341651 CTTTATGTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
20 3 0.07
21 14 0.33
22 2 0.05
23 6 0.14
25 6 0.14
26 2 0.05
27 7 0.16
28 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (21 bp):
AATGCATATGTCTAATTGTCG
Found at i:342131 original size:18 final size:18
Alignment explanation
Indices: 342101--342142 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
342091 AGGGTCTACA
* *
342101 TGGT-CTTCGGGACATAG
1 TGGTCCTTCAGGACACAG
342118 TGGTCCTTCAGGACACAG
1 TGGTCCTTCAGGACACAG
342136 TGGTCCT
1 TGGTCCT
342143 ACGGGACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.17, C:0.24, G:0.31, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCAGGACACAG
Found at i:342149 original size:18 final size:18
Alignment explanation
Indices: 342108--342150 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
342098 ACATGGTCTT
* *
342108 CGGGACATAGTGGTCCTT
1 CGGGACACAGTGGTCCTA
*
342126 CAGGACACAGTGGTCCTA
1 CGGGACACAGTGGTCCTA
342144 CGGGACA
1 CGGGACA
342151 AATTCTACGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19
Consensus pattern (18 bp):
CGGGACACAGTGGTCCTA
Found at i:345865 original size:22 final size:23
Alignment explanation
Indices: 345840--345893 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
345830 AATATTTATA
345840 AATTAAATTTA-A-ACAAAAATTC
1 AATTAAATTTACAGA-AAAAATTC
*
345862 AATTAATTTTACTAGAAAAAATTC
1 AATTAAATTTAC-AGAAAAAATTC
345886 AATTAAAT
1 AATTAAAT
345894 AGGATAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
24 16 0.59
25 1 0.04
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATTTACAGAAAAAATTC
Found at i:346602 original size:37 final size:37
Alignment explanation
Indices: 346542--346617 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
346532 ATTACGCAAC
* ** *
346542 CAAAAATATGACTGCAACCGTGATTTAAATCTCTAAA
1 CAAAAATACGACCACAACAGTGATTTAAATCTCTAAA
346579 CAAAAATACGACCACAACAGTGATTTAAATCTCTAAA
1 CAAAAATACGACCACAACAGTGATTTAAATCTCTAAA
346616 CA
1 CA
346618 TAATTGCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (37 bp):
CAAAAATACGACCACAACAGTGATTTAAATCTCTAAA
Found at i:352127 original size:19 final size:21
Alignment explanation
Indices: 352105--352151 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
352095 AAATTAAAAA
*
352105 ATATCATGAAAATATA-T-TT
1 ATATCATAAAAATATATTCTT
*
352124 ATATTATAAAAATATATTCTT
1 ATATCATAAAAATATATTCTT
352145 ATATCAT
1 ATATCAT
352152 TTTATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 14 0.61
20 1 0.04
21 8 0.35
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATCATAAAAATATATTCTT
Found at i:352822 original size:33 final size:33
Alignment explanation
Indices: 352783--352861 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
352773 GTCTGCATGT
352783 GCCATGCACGTCCCCAACACCCCAACACAGGTC
1 GCCATGCACGTCCCCAACACCCCAACACAGGTC
* *
352816 TCCATGCACGTCCCCAGCACCCCAACACAGGTC
1 GCCATGCACGTCCCCAACACCCCAACACAGGTC
352849 GCCATGCAC-TCCC
1 GCCATGCACGTCCC
352862 AGCGACCTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 4 0.09
33 39 0.91
ACGTcount: A:0.24, C:0.49, G:0.15, T:0.11
Consensus pattern (33 bp):
GCCATGCACGTCCCCAACACCCCAACACAGGTC
Found at i:352934 original size:22 final size:22
Alignment explanation
Indices: 352906--352968 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
352896 CCAAGCTTAG
*
352906 GACCAAACTTATCCCTGGTGGC
1 GACCAAACTTATCCCTGCTGGC
352928 GACCAAACTTATCCCTGCTGGC
1 GACCAAACTTATCCCTGCTGGC
*
352950 GACCAAACTTAACCCTGCT
1 GACCAAACTTATCCCTGCT
352969 CCCTCGTGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.22
Consensus pattern (22 bp):
GACCAAACTTATCCCTGCTGGC
Found at i:353013 original size:23 final size:23
Alignment explanation
Indices: 352983--353027 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
352973 CGTGCATGGG
352983 TTGCATCCATAGCTGGGAGATTC
1 TTGCATCCATAGCTGGGAGATTC
353006 TTGCATCCATAGCTGGGAGATT
1 TTGCATCCATAGCTGGGAGATT
353028 GTAGCCAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (23 bp):
TTGCATCCATAGCTGGGAGATTC
Found at i:353491 original size:28 final size:30
Alignment explanation
Indices: 353451--353512 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
353441 AATTTAGTTA
353451 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
353479 ATTAGTTTGTTAGTTTAAGTTATATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
353509 ATTA
1 ATTA
353513 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAGTTTAAGTTATATATTAT
Found at i:353849 original size:20 final size:21
Alignment explanation
Indices: 353805--353849 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
353795 AAATATTGTG
**
353805 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
353826 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
353846 TTTA
1 TTTA
353850 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:357078 original size:10 final size:10
Alignment explanation
Indices: 357063--357089 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
357053 AATGATTTGA
357063 TAGTAATGAT
1 TAGTAATGAT
357073 TAGTAATGAT
1 TAGTAATGAT
357083 TAGTAAT
1 TAGTAAT
357090 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:357113 original size:21 final size:22
Alignment explanation
Indices: 357089--357138 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
357079 TGATTAGTAA
357089 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
357110 TAATGATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
*
357132 TAGTAAT
1 TAATAAT
357139 GATTTACGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:357118 original size:58 final size:60
Alignment explanation
Indices: 357010--357142 Score: 216
Period size: 58 Copynumber: 2.2 Consensus size: 60
357000 GTATTTATAA
* *
357010 GATTTAGTAATTATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
357070 GA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
357128 GATTTAGTAATGATT
1 GATTTAGTAATGATT
357143 TACGACTTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
58 34 0.50
59 32 0.47
60 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:357280 original size:60 final size:60
Alignment explanation
Indices: 357216--357522 Score: 467
Period size: 60 Copynumber: 5.3 Consensus size: 60
357206 GAAATTATAA
*
357216 TAATGATTTAGTAATGGTTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
* * *
357276 TAATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
357336 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
*
357396 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--AT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
* *
357449 T--TGA--TAGTAATGACTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
357504 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
357523 TGATAGTAAT
Statistics
Matches: 224, Mismatches: 12, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
48 13 0.06
49 22 0.10
51 4 0.02
52 1 0.00
53 5 0.02
55 5 0.02
56 1 0.00
57 4 0.02
59 13 0.06
60 156 0.70
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:357495 original size:48 final size:49
Alignment explanation
Indices: 357404--357518 Score: 178
Period size: 48 Copynumber: 2.3 Consensus size: 49
357394 ATTAATGATT
*
357404 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* *
357453 TAGTAATGACTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
357501 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
357519 GATTTGATAG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 34 0.57
49 26 0.43
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:357506 original size:14 final size:14
Alignment explanation
Indices: 357490--357537 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
357480 TATTAATATT
*
357490 TAATGATTTGATAT
1 TAATGATTTGATAG
357504 TAATGA-TT--TAG
1 TAATGATTTGATAG
357515 TAATGATTTGATAG
1 TAATGATTTGATAG
357529 TAATGATTT
1 TAATGATTT
357538 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:357519 original size:25 final size:25
Alignment explanation
Indices: 357490--357538 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
357480 TATTAATATT
*
357490 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
357515 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
357539 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:357635 original size:21 final size:21
Alignment explanation
Indices: 357611--357751 Score: 55
Period size: 21 Copynumber: 6.7 Consensus size: 21
357601 GAAATTATAA
357611 TAATGATTTAGTAATGATTAG
1 TAATGATTTAGTAATGATTAG
* * * *
357632 TAAT-A-AT-GAAATTATTAT
1 TAATGATTTAGTAATGATTAG
* * * * *
357650 TAAT-ATTTAATGATTTAATAT
1 TAATGATTTAGT-AATGATTAG
357671 TAATGATTTAGTAATGATTAG
1 TAATGATTTAGTAATGATTAG
* *
357692 TAATAATGAGTTATTAAT-ATT--
1 ---TAATGATTTAGTAATGATTAG
357713 TAATGATTTGATAGTAATGATTTAG
1 TAATGA-TT--TAGTAATGA-TTAG
357738 TAATGA-TTAGTAAT
1 TAATGATTTAGTAAT
357752 AATGAAATTA
Statistics
Matches: 88, Mismatches: 18, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
18 19 0.22
19 3 0.03
20 1 0.01
21 33 0.38
22 7 0.08
23 6 0.07
24 13 0.15
25 6 0.07
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (21 bp):
TAATGATTTAGTAATGATTAG
Found at i:357675 original size:14 final size:14
Alignment explanation
Indices: 357649--357736 Score: 58
Period size: 14 Copynumber: 6.2 Consensus size: 14
357639 GAAATTATTA
357649 TTAATATTTAATGAT
1 TTAATA-TTAATGAT
357664 TTAATATTAATGA-
1 TTAATATTAATGAT
*
357677 TT--TAGTAATGA-
1 TTAATATTAATGAT
* *
357688 TTAGTAATAATGAGTT
1 TTAATATTAATGA--T
357704 ATTAATATTTAATGAT
1 -TTAATA-TTAATGAT
* *
357720 TTGATAGTAATGAT
1 TTAATATTAATGAT
357734 TTA
1 TTA
357737 GTAATGATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
11 10 0.17
13 10 0.17
14 16 0.27
15 11 0.19
16 1 0.02
17 5 0.08
18 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (14 bp):
TTAATATTAATGAT
Found at i:357678 original size:60 final size:60
Alignment explanation
Indices: 357611--357923 Score: 530
Period size: 60 Copynumber: 5.3 Consensus size: 60
357601 GAAATTATAA
*
357611 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
* *
357671 TAATGATTTAGTAATGATTAGTAATAATG--A--GTTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
357727 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
* *
357787 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
*
357847 TAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
357905 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
357924 TACGACTTGA
Statistics
Matches: 238, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
56 52 0.22
58 36 0.15
59 33 0.14
60 117 0.49
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:357687 original size:11 final size:11
Alignment explanation
Indices: 357671--357751 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 11
357661 GATTTAATAT
357671 TAATGATTTAG
1 TAATGATTTAG
*
357682 TAATGATTAGTAA
1 TAATGATT--TAG
* *
357695 TAATGAGTTAT
1 TAATGATTTAG
357706 TAAT-A-TT--
1 TAATGATTTAG
357713 TAATGATTTGATAG
1 TAATGA-TT--TAG
357727 TAATGATTTAG
1 TAATGATTTAG
357738 TAATGA-TTAG
1 TAATGATTTAG
357748 TAAT
1 TAAT
357752 AATGAAATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 19
0.73 0.04 0.24
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 2 0.03
10 10 0.17
11 23 0.40
12 1 0.02
13 11 0.19
14 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
TAATGATTTAG
Found at i:357737 original size:116 final size:118
Alignment explanation
Indices: 357611--357923 Score: 544
Period size: 116 Copynumber: 2.7 Consensus size: 118
357601 GAAATTATAA
*
357611 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
*
357676 ATTTAGTAATGATTAGTAATAATG-A-GTTATTAATATTTAATGATTTGATAG
66 ATTTAGTAATGATTAGTAATAATGAATATTATTAATATTTAATGATTTGATAG
357727 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
*
357792 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
66 ATTTAGTAATGATTAGTAATAATG-AA-TATTATTAATATTTAATGATTTGATAG
*
357847 TAATGA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
357910 ATTTAGTAATGATT
66 ATTTAGTAATGATT
357924 TACGACTTGA
Statistics
Matches: 189, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
116 88 0.47
118 50 0.26
119 21 0.11
120 30 0.16
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (118 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
ATTTAGTAATGATTAGTAATAATGAATATTATTAATATTTAATGATTTGATAG
Found at i:357809 original size:391 final size:388
Alignment explanation
Indices: 357010--358006 Score: 1702
Period size: 391 Copynumber: 2.6 Consensus size: 388
357000 GTATTTATAA
* * *
357010 GATTTAGTAATTATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
357075 GTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATG
66 GTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTT-ATATTAATGATTTAGTAATG
357140 ATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATA-TTTCGTTACATAACTAGTA
130 ATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTA
*
357204 ATGAAATTATAATAATGATTTAGTAATGGTTAGTAATAATGAAATTATTATTAATATTTAATGAT
195 ATGAAATTATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGAT
*
357269 TTGATATTAATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAT
260 TTAATATTAATGATTTAATAATGATTAGTAATAATG-AA-TGTTATTAATATTTAATGATTTGAT
357334 AGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
323 AGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA
357399 T
388 T
357400 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGACTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-T-
* * * * * * *
357465 GTAATAATAATTTATTATTAAT-ATTTAATGATTTGATA-TTAATGA-TT-TAGTAATGATTTGA
64 -TAGTAATGA-TTAGTAATAATAATTT-ATTA-TTAATATTTAATGATTTATATTAATGA-TT--
*
357526 TAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAATCATATTTTCGTTACAT
122 TAGTAATGATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACAT
357591 AACTAGTAATGAAATTATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATAT
187 AACTAGTAATGAAATTATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATAT
*
357656 TTAATGATTTAATATTAATGATTTAGTAATGATTAGTAATAATG-A-GTTATTAATATTTAATGA
252 TTAATGATTTAATATTAATGATTTAATAATGATTAGTAATAATGAATGTTATTAATATTTAATGA
357719 TTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
317 TTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
357784 TATTAAT
382 TATTAAT
357791 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
357856 GTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATG
66 GTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTT-ATATTAATGATTTAGTAATG
357921 ATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTA
130 ATTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTA
357986 ATGAAATTATAATAATGATTT
195 ATGAAATTATAATAATGATTT
358007 GATACTAAAA
Statistics
Matches: 570, Mismatches: 22, Indels: 33
0.91 0.04 0.05
Matches are distributed among these distances:
386 5 0.01
387 112 0.20
388 13 0.02
389 2 0.00
390 68 0.12
391 161 0.28
392 2 0.00
393 14 0.02
394 71 0.12
395 122 0.21
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (388 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
GTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTATATTAATGATTTAGTAATGA
TTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTAA
TGAAATTATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATT
TAATATTAATGATTTAATAATGATTAGTAATAATGAATGTTATTAATATTTAATGATTTGATAGT
AATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
Found at i:357857 original size:10 final size:10
Alignment explanation
Indices: 357844--357870 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
357834 AATGATTTGA
357844 TAGTAATGAT
1 TAGTAATGAT
357854 TAGTAATGAT
1 TAGTAATGAT
357864 TAGTAAT
1 TAGTAAT
357871 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:357894 original size:21 final size:22
Alignment explanation
Indices: 357870--357919 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
357860 TGATTAGTAA
357870 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
357891 TAATGATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
*
357913 TAGTAAT
1 TAATAAT
357920 GATTTACGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:360158 original size:15 final size:14
Alignment explanation
Indices: 360135--360165 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
360125 TACAACACTA
360135 AACTTTAATATAAT
1 AACTTTAATATAAT
360149 AACTTATAATATAAT
1 AACTT-TAATATAAT
360164 AA
1 AA
360166 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:360173 original size:16 final size:16
Alignment explanation
Indices: 360140--360186 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
360130 CACTAAACTT
*
360140 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
360155 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
360171 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
360187 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:360668 original size:13 final size:13
Alignment explanation
Indices: 360629--360675 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
360619 CTCACAAGAG
360629 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
360643 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
360657 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
360670 -CTTTCT
1 CCTTTCT
360676 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:360720 original size:26 final size:26
Alignment explanation
Indices: 360682--360732 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
360672 TTCTTTCTCG
*
360682 GCTGCAATTTCTTCTCCCTTTCTTTT
1 GCTGCAATCTCTTCTCCCTTTCTTTT
360708 GCTGCAATCTCTTCTCCCTTTCTTT
1 GCTGCAATCTCTTCTCCCTTTCTTT
360733 CTTTTATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.08, C:0.33, G:0.08, T:0.51
Consensus pattern (26 bp):
GCTGCAATCTCTTCTCCCTTTCTTTT
Found at i:361021 original size:29 final size:29
Alignment explanation
Indices: 360939--361026 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
360929 AGGAAAGCTT
* * * ***
360939 GTCGCCGGGACTGCTTGGCGACCTACAAG
1 GTCGCTGGGAGTGCATGGCGACCTTGTAG
360968 GTCGCTGGGAGTGCATGGCGACCTTGTAG
1 GTCGCTGGGAGTGCATGGCGACCTTGTAG
360997 GTCGCTGGGAGTGCATGGCGACCTTGTAG
1 GTCGCTGGGAGTGCATGGCGACCTTGTAG
361026 G
1 G
361027 GGTATTGGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.15, C:0.24, G:0.40, T:0.22
Consensus pattern (29 bp):
GTCGCTGGGAGTGCATGGCGACCTTGTAG
Found at i:361046 original size:31 final size:31
Alignment explanation
Indices: 360974--361069 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 31
360964 CAAGGTCGCT
*
360974 GGGAGTGCATGGCGACCTTGTA--GGTCGCT-
1 GGGAGTGCATGGCGACCTTGTAGGGGT-GTTG
*
361003 GGGAGTGCATGGCGACCTTGTAGGGGTATTG
1 GGGAGTGCATGGCGACCTTGTAGGGGTGTTG
* *
361034 GGGAATGCATGGCGACCTGTGTTGGGGTGTTG
1 GGGAGTGCATGGCGACCT-TGTAGGGGTGTTG
361066 GGGA
1 GGGA
361070 CGTGAATGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
29 22 0.38
30 1 0.02
31 20 0.34
32 15 0.26
ACGTcount: A:0.15, C:0.15, G:0.46, T:0.25
Consensus pattern (31 bp):
GGGAGTGCATGGCGACCTTGTAGGGGTGTTG
Found at i:363907 original size:29 final size:29
Alignment explanation
Indices: 363850--363904 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
363840 TACTAAAACG
* *
363850 AATCAAATCTGATAGTTTACATACTAATA
1 AATCAAAACTGATAATTTACATACTAATA
*
363879 AATCAAAACT-ATAATTTAGATACTAA
1 AATCAAAACTGATAATTTACATACTAA
363905 ATACATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (29 bp):
AATCAAAACTGATAATTTACATACTAATA
Found at i:368762 original size:24 final size:24
Alignment explanation
Indices: 368710--368762 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
368700 TAGGTTTAAT
*
368710 TAATAGTACACCACATTAAAACAA
1 TAATAGTACACAACATTAAAACAA
* * * *
368734 CAATAGTACATAACATTATAATAA
1 TAATAGTACACAACATTAAAACAA
368758 TAATA
1 TAATA
368763 ATAATAATAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (24 bp):
TAATAGTACACAACATTAAAACAA
Found at i:371881 original size:76 final size:77
Alignment explanation
Indices: 371754--371910 Score: 298
Period size: 76 Copynumber: 2.1 Consensus size: 77
371744 GCTAACCCTA
*
371754 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAGCAGTGTCAGCAATACACTTGTACTCA
1 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAACAGTGTCAGCAATACACTTGTACTCA
371819 GCTTCCATTATG
66 GCTTCCATTATG
371831 GATCAGCAAGTAAGGCACTTA-CCATGTTACTTCAGCAACAGTGTCAGCAATACACTTGTACTCA
1 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAACAGTGTCAGCAATACACTTGTACTCA
371895 GCTTCCATTATG
66 GCTTCCATTATG
371907 GATC
1 GATC
371911 TGGACACTGA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
76 58 0.73
77 21 0.27
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (77 bp):
GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAACAGTGTCAGCAATACACTTGTACTCA
GCTTCCATTATG
Found at i:376748 original size:28 final size:29
Alignment explanation
Indices: 376712--376789 Score: 106
Period size: 31 Copynumber: 2.7 Consensus size: 29
376702 GGTAAGATAT
376712 AATTAATCATAGGAAATG-TACAAAATA-
1 AATTAATCATAGGAAATGATACAAAATAG
376739 ATATTAATCATAGGAAATGGGATACAAAATAG
1 A-ATTAATCATAGGAAAT--GATACAAAATAG
*
376771 AATTAATCATAAGAAATGA
1 AATTAATCATAGGAAATGA
376790 GGTGAGGTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 1 0.02
28 16 0.36
29 2 0.04
30 1 0.02
31 24 0.53
32 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (29 bp):
AATTAATCATAGGAAATGATACAAAATAG
Found at i:382976 original size:30 final size:30
Alignment explanation
Indices: 382907--382974 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
382897 CATGGTCCCC
382907 TAAAATTTT-AAAAATCATAATTTAGACCGT
1 TAAAATTTTAAAAAAT-ATAATTTAGACCGT
*
382937 TAAAATTTTAAAAAAT-TAATTT-GACCCTT
1 TAAAATTTTAAAAAATATAATTTAGA-CCGT
382966 TAAAATTTT
1 TAAAATTTT
382975 TAGAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 2 0.06
29 18 0.51
30 9 0.26
31 6 0.17
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAAATTTTAAAAAATATAATTTAGACCGT
Found at i:387203 original size:2 final size:2
Alignment explanation
Indices: 387198--387260 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
387188 ATAAAAAATA
387198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
387240 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
387261 GAAAATCATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:389014 original size:256 final size:256
Alignment explanation
Indices: 388578--389424 Score: 1080
Period size: 256 Copynumber: 3.3 Consensus size: 256
388568 TTCCTCATGA
* * * * * * * *
388578 TTGAGTCGATCTTGGATGACTTGAGCATGAT-TTCCTTTATCGTGAAGTTGAAATCTAGCTCGAA
1 TTGAGTCGATATTGGGTGATTTAAGCATGATATT-CTTCATTGTGAAGTTGAAATCAAGCTCAAA
* * * * *
388642 CTCTGAACCAGAAAGTAGTTCCTCATTATTGAGTTAACCTAAATCACAATTGATTTTTGGGTCTT
65 ATCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGA-TTTTGGGTCTT
* *
388707 CTTCTAGTCCAATATCATTCATC-GTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
129 ATTCTAGTCCAATATCCTT-ATCTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* *
388771 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCATGGCCGACTCCTTCTTTGTGAAG
193 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * *
388835 TTAAGTTGATATTGGGTGATTTAAGCATGATATTCTTCGTTGTGAAGTTGAAATCAAGCTCAAAA
1 TTGAGTCGATATTGGGTGATTTAAGCATGATATTCTTCATTGTGAAGTTGAAATCAAGCTCAAAA
* * * * * *
388900 TCTGAACTGGAAAGTAGCTCCCCGTTGTTGAGTTAAGCTAAATTACATTTGATTTTGGGTCTTAT
66 TCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGATTTTGGGTCTTAT
* *
388965 TCTAGTCCAATATCCTTAGCTGTGAAGTTAAAATTTGACTTGAAGACCTTGGTTTAAAAATTA-C
131 TCTAGTCCAATATCCTTATCTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAA-TAGC
* * * * *
389029 TCCCTGAGCACGATATCCTTTATTATAAAGTTGAAATCGTGGTCGACTCCTTCGTTGTGAAG
195 TCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * * * *
389091 TTGAGTCGATCTTGGGTGATTTGAA-CATGATATACTTCATCGTGAAGTTGAAAACAAGGTCAAA
1 TTGAGTCGATATTGGGTGATTT-AAGCATGATATTCTTCATTGTGAAGTTGAAATCAAGCTCAAA
* * * *
389155 ATCTGAACTGGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCGCAATTGATTTTGGGTATTT
65 ATCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGATTTTGGGTCTTA
* *
389220 TTCTAGTCCAATA-CCTT-TCGTCGTGAAGTTGAAATTTGGCTTGAAGACCTTGGTTTGAAAATA
130 TTCTAGTCCAATATCCTTATC-T-GTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* * * *
389283 GCTCCATGAGCATGATATCTTTCATCATGAAGTTGAAATTGTGGCCGACTCCTTCGCTGTGAAG
193 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * * * *
389347 TTGAGTCGATATTGGATGATTTGAGTATGATA-TCATT-TTTCGTGAAGTTGAAATCAAGCTCGA
1 TTGAGTCGATATTGGGTGATTTAAGCATGATATTC-TTCATT-GTGAAGTTGAAATCAAGCTCAA
389410 AATCTGAACTAGAAA
64 AATCTGAACTAGAAA
389425 ATGGCTTATT
Statistics
Matches: 508, Mismatches: 72, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
254 1 0.00
255 12 0.02
256 396 0.78
257 97 0.19
258 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (256 bp):
TTGAGTCGATATTGGGTGATTTAAGCATGATATTCTTCATTGTGAAGTTGAAATCAAGCTCAAAA
TCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGATTTTGGGTCTTAT
TCTAGTCCAATATCCTTATCTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATAGCT
CCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
Found at i:389505 original size:256 final size:253
Alignment explanation
Indices: 388578--389527 Score: 954
Period size: 256 Copynumber: 3.7 Consensus size: 253
388568 TTCCTCATGA
* * * * * * *
388578 TTGAGTCGATCTTGGATGACTTGAGCATGATTTCCTT-TATCGTGAAGTTGAAATCTAGCTCGAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATATCATTCT-TCGTGAAGTTGAAATCAAGCTCAAA
* ** * * * **
388642 CTCTGAACCAGAAAGTAGTTCCTCATT-ATTGAGTTAACCTAAATCACAATTGATTTTTGGGTCT
65 ATCTGAACTGGAAAGT-G--GCTCATTGTTTGAGTTAAGCTAAATTGCAATTGA-TTTTGGGTCT
* * *
388706 -TCTTCTAGTCCAATATCATTCATCGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAAT
126 AT-TT-TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAAT
* * *
388770 AGCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCATGGCCGACTCCTTCTTTGTGAAG
189 AGCTCCATGAGCACGATATCTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * *
388835 TTAAGTTGATATTGGGTGATTTAAGCATGATATTC-TTCGTT-GTGAAGTTGAAATCAAGCTCAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATA-TCATTC-TTCGTGAAGTTGAAATCAAGCTCAA
* * * *
388898 AATCTGAACTGGAAAGTAGCTCCCCGTTG-TTGAGTTAAGCTAAATTACATTTGATTTTGGGTCT
64 AATCTGAACTGGAAAGTGGCT---CATTGTTTGAGTTAAGCTAAATTGCAATTGATTTTGGGTC-
* * * *
388962 TATTCTAGTCCAATATCCTTAGCTGTGAAGTTAAAATTTGACTTGAAGACCTTGGTTTAAAAATT
125 TATTTTAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAA-T
* * * *
389027 A-CTCCCTGAGCACGATATCCTTT-ATTATAAAGTTGAAATCGTGGTCGACTCCTTCGTTGTGAA
189 AGCTCCATGAGCACGATAT-CTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAA
389090 G
253 G
* * * * *
389091 TTGAGTCGATCTTGGGTGATTTGAACATGATAT-ACTTCATCGTGAAGTTGAAAACAAGGTCAAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATATCA-TTCTTCGTGAAGTTGAAATCAAGCTCAAA
* * * *
389155 ATCTGAACTGGAAAGTAGATCCTCATTG-TTGAGTTAAGCTAAATCGCAATTGATTTTGGGTATT
65 ATCTGAACTGGAAAGT-G--GCTCATTGTTTGAGTTAAGCTAAATTGCAATTGATTTTGGGTCTA
* * *
389219 TTTCTAGTCCAATA-CCTTTCGTCGTGAAGTTGAAATTTGGCTTGAAGACCTTGGTTTGAAAATA
127 TTT-TAGTCCAATATCC-TTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* * *
389283 GCTCCATGAGCATGATATCTTTCATCATGAAGTTGAAATTGTGGCCGACTCCTTCGCTGTGAAG
190 GCTCCATGAGCACGATATCTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * * *
389347 TTGAGTCGATATTGGATGATTTGAGTATGATATCATTTTTCGTGAAGTTGAAATCAAGCTCGAAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATATCATTCTTCGTGAAGTTGAAATCAAGCTCAAAA
* * * ** * * * * *
389412 TCTGAACTAGAAAATGGCTTATTGTTATCGAGTTGAA-CTAGTTTGTAGTTGATTTCGGATCTCC
66 TCTGAACTGGAAAGTGGCTCATTGTT-T-GAGTT-AAGCTAAATTGCAATTGATTTTGGGTCT-A
* * * *
389476 TTTTAG-CCTAATATCCTTCGTTATGAAGTTGAAATTCGGCTTGAACACCTTG
127 TTTTAGTCC-AATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTG
389528 ATGATAGCTC
Statistics
Matches: 576, Mismatches: 88, Indels: 59
0.80 0.12 0.08
Matches are distributed among these distances:
253 6 0.01
254 3 0.01
255 17 0.03
256 442 0.77
257 101 0.18
258 4 0.01
259 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (253 bp):
TTGAGTCGATATTGGGTGATTTGAGCATGATATCATTCTTCGTGAAGTTGAAATCAAGCTCAAAA
TCTGAACTGGAAAGTGGCTCATTGTTTGAGTTAAGCTAAATTGCAATTGATTTTGGGTCTATTTT
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATAGCTCCA
TGAGCACGATATCTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
Found at i:401400 original size:15 final size:15
Alignment explanation
Indices: 401380--401413 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
401370 TCAAGATTAT
**
401380 TTAAACATATGTATA
1 TTAAACATACATATA
401395 TTAAACATACATATA
1 TTAAACATACATATA
401410 TTAA
1 TTAA
401414 CTCTAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAACATACATATA
Found at i:405746 original size:6 final size:6
Alignment explanation
Indices: 405735--405764 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
405725 TTAGCATCTT
405735 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
405765 CAAAGAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:405805 original size:21 final size:21
Alignment explanation
Indices: 405758--405805 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
405748 AAAAATAAAA
405758 ATAAAAACAAAGAAAACTTTG
1 ATAAAAACAAAGAAAACTTTG
* *
405779 A-AAAAAGAAAAGAAAACTTTT
1 ATAAAAA-CAAAGAAAACTTTG
405800 ATAAAA
1 ATAAAA
405806 CTCAAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
ATAAAAACAAAGAAAACTTTG
Found at i:409707 original size:10 final size:9
Alignment explanation
Indices: 409676--409705 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
409666 ATTTTATACA
409676 TTACATTCT
1 TTACATTCT
409685 TTATCATTCT
1 TTA-CATTCT
409695 TTACATTCT
1 TTACATTCT
409704 TT
1 TT
409706 TATTTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (9 bp):
TTACATTCT
Found at i:410823 original size:64 final size:65
Alignment explanation
Indices: 410718--410882 Score: 203
Period size: 64 Copynumber: 2.6 Consensus size: 65
410708 TTTCAAAGTA
* **
410718 GTGTACCAATGCACCA-ATCAATGCATCGATGCA-TCCTTGAATAAATTGAATTTCGAATGCATT
1 GTGTACCAATGCA-CAGA-CCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATT
410781 TT
64 TT
* * * **
410783 GTGTACCGATGCACA-AGGCATGCATCAATGCACTCC-TGAATATTTTGAACATCGAATGCATTT
1 GTGTACCAATGCACAGA-CCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTT
410846 T
65 T
410847 GTGTACCAATGCACAGACCATGCATCGATGCACTCC
1 GTGTACCAATGCACAGACCATGCATCGATGCACTCC
410883 AGCTTGTTTG
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 70 0.81
65 16 0.19
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (65 bp):
GTGTACCAATGCACAGACCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTT
Found at i:413041 original size:21 final size:22
Alignment explanation
Indices: 413003--413043 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
412993 AAGACTTTAT
413003 TTTCAAAATATAAAAAATGATA
1 TTTCAAAATATAAAAAATGATA
*
413025 TTTCAAAAT-TGAAAAATGA
1 TTTCAAAATATAAAAAATGA
413044 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
TTTCAAAATATAAAAAATGATA
Found at i:416931 original size:23 final size:22
Alignment explanation
Indices: 416852--416929 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
416842 ACTAGCTAGT
*
416852 GCATCGATGCATCCCTTGAATGT
1 GCATCGATGCAT-CCTTGAATGA
* *
416875 GCATCGATACAT-CATGAA-GA
1 GCATCGATGCATCCTTGAATGA
*
416895 TGCACCGATGCACTCCTTGAATGA
1 -GCATCGATGCA-TCCTTGAATGA
416919 GCATCGATGCA
1 GCATCGATGCA
416930 CTATGCTGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.32
22 1 0.02
23 26 0.59
24 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (22 bp):
GCATCGATGCATCCTTGAATGA
Found at i:419669 original size:64 final size:65
Alignment explanation
Indices: 419519--419682 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 65
419509 TTCAAAGTAG
* * * **
419519 TGTACCGATGCACCAATCAATGCATCGAAGCA-TCCTTGAATAAATTGAATTTCGAATGCATTTT
1 TGTACCGATGCA-CAAGCCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTT
*
419583 G
65 A
* * **
419584 TGTACCGATGTACAAGGCATGCATCGATGCACTCC-TGAATATTTTGAACATCGAATGCATTTTA
1 TGTACCGATGCACAAGCCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTTA
* *
419648 TGTACCGATGCACATA-CCATGCATCTATGTACTCC
1 TGTACCGATGCACA-AGCCATGCATCGATGCACTCC
419683 AGCTTGTTTG
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 68 0.82
65 15 0.18
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (65 bp):
TGTACCGATGCACAAGCCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTTA
Found at i:421234 original size:7 final size:7
Alignment explanation
Indices: 421222--421333 Score: 68
Period size: 7 Copynumber: 16.0 Consensus size: 7
421212 ACCTAAAGAG
421222 GAAAAAA
1 GAAAAAA
421229 GAAAAAAA
1 G-AAAAAA
421237 GAAAAAA
1 GAAAAAA
*
421244 -AAAGAA
1 GAAAAAA
*
421250 CAAGAAAA
1 GAA-AAAA
* *
421258 G-AACAG
1 GAAAAAA
*
421264 GAAAAAT
1 GAAAAAA
*
421271 GAAAAAT
1 GAAAAAA
*
421278 GAAAAAT
1 GAAAAAA
*
421285 GAAAAAG
1 GAAAAAA
421292 GAAAAAA
1 GAAAAAA
421299 GAAAAAA
1 GAAAAAA
* *
421306 TAAATAA
1 GAAAAAA
**
421313 -AAAATG
1 GAAAAAA
421319 GAAAAAA
1 GAAAAAA
421326 GGAAAAAA
1 -GAAAAAA
421334 TAGAAGGAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
6 11 0.13
7 55 0.66
8 17 0.20
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (7 bp):
GAAAAAA
Found at i:421236 original size:8 final size:8
Alignment explanation
Indices: 421223--421338 Score: 54
Period size: 8 Copynumber: 13.1 Consensus size: 8
421213 CCTAAAGAGG
421223 AAAAAAGA
1 AAAAAAGA
421231 AAAAAAGA
1 AAAAAAGA
421239 AAAAAA-A
1 AAAAAAGA
*
421246 AGAACAAGA
1 A-AAAAAGA
*
421255 AAAGAACAGG
1 AAA-AA-AGA
*
421265 AAAAATGA
1 AAAAAAGA
*
421273 AAAATGAAAA
1 AAAA--AAGA
*
421283 ATGAAAAAGG
1 A--AAAAAGA
421293 AAAAAAGA
1 AAAAAAGA
*
421301 AAAAATAAA
1 AAAAA-AGA
421310 TAAAAAATGGA
1 -AAAAAA--GA
*
421321 AAAAAGGA
1 AAAAAAGA
421329 AAAAATAGA
1 AAAAA-AGA
421338 A
1 A
421339 GGAAGAAAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
7 2 0.02
8 43 0.53
9 11 0.14
10 21 0.26
11 1 0.01
12 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.06
Consensus pattern (8 bp):
AAAAAAGA
Found at i:421236 original size:10 final size:11
Alignment explanation
Indices: 421230--421262 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
421220 AGGAAAAAAG
421230 AAAAAAAGAA-
1 AAAAAAAGAAC
421240 AAAAAAAGAAC
1 AAAAAAAGAAC
*
421251 AAGAAAAGAAC
1 AAAAAAAGAAC
421262 A
1 A
421263 GGAAAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAC
Found at i:423933 original size:117 final size:118
Alignment explanation
Indices: 423734--423947 Score: 324
Period size: 117 Copynumber: 1.8 Consensus size: 118
423724 TCCATCATAG
* * * *
423734 AAGGAGGTGGATCATCATTTCCAATGGAGGGGTTTATAATGAGAAGAACTCGTCCGATGAGGGAG
1 AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
* *
423799 AAGAAGTTCATAATGAGATGAACTTGTTCAACTTTTGTTCGAATACATCACAA
66 AAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTGTTCGAATACATCACAA
* *
423852 AAGGAGGTGGATCAAT-ATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATTCGATAAGGGA
1 AAGGAGGTGGATC-ATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGA
*
423915 GAAGAAGTTTATAATGAGAAGAAATTGTTCAAC
65 GAAGAAGTTCATAATGAGAAGAAATTGTTCAAC
423948 CTTAGCTCGA
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 60 0.70
118 24 0.28
119 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (118 bp):
AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
AAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTGTTCGAATACATCACAA
Found at i:423973 original size:117 final size:118
Alignment explanation
Indices: 423734--423974 Score: 315
Period size: 117 Copynumber: 2.1 Consensus size: 118
423724 TCCATCATAG
* * * *
423734 AAGGAGGTGGATCATCATTTCCAATGGAGGGGTTTATAATGAGAAGAACTCGTCCGATGAGGGAG
1 AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
* * * * * *
423799 AAGAAGTTCATAATGAGATGAACTTGTTCAACTTTTGTTCGAATACATCACAA
66 AAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGAATACAACACAA
* *
423852 AAGGAGGTGGATCAAT-ATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATTCGATAAGGGA
1 AAGGAGGTGGATC-ATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGA
* * * *
423915 GAAGAAGTTTATAATGAGAAGAAATTGTTCAACCTTAGCTCGATTCCAACACAT
65 GAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGAATACAACACAA
423969 AAGGAG
1 AAGGAG
423975 TTAGAATAGC
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
117 80 0.75
118 24 0.23
119 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (118 bp):
AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
AAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGAATACAACACAA
Found at i:424336 original size:118 final size:118
Alignment explanation
Indices: 424161--424774 Score: 677
Period size: 118 Copynumber: 5.2 Consensus size: 118
424151 TCATCACTTC
* * * * * *
424161 GTTCGAATCCATCACAGGAGGATGTGGATCAA-AATTTCTAATGGGAGAGTTCATAATGAGAAGA
1 GTTCGAATCCATCACAGAAGGAGGTAGATCAACATTTTC-AATGGAAGGGTTCATAATGAGAAGA
*
424225 ACTCATCCGAAGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
65 ACTCATCCGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * **
424279 GTTCAAATCCATCATAGAATAAGGT-GTATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
1 GTTCGAATCCATCACAGAAGGAGGTAG-ATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
* * * * *
424343 ACTAAT-TGAATGTGGGAGAAGAAGTTTATAATGAAAAGAACTTGTTCAACCTTT
65 ACTCATCCGAA-GAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * * * *
424397 GTTCGATTCCATCACCGGAGTAGATGGAAT-AACATTTTCAATGGAAGGGTTCATAATGAGAAGA
1 GTTCGAATCCATCACAGAAGGAGGTAG-ATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
* * * *
424461 ACTCATCTGAAGAGGGAGAAAAACGTTAATAATGAGAAGAACTTGTTTAACCTTT
65 ACTCATCCGAAGAGGGAGAAGAA-GTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * * * * * * *
424516 ATTTGATTCAATCACAGGAGGAGGTAGATCAACATTTCCAATGGGAGAGTTCATAATGTA-TAGA
1 GTTCGAATCCATCACAGAAGGAGGTAGATCAACATTTTCAATGGAAGGGTTCATAATG-AGAAGA
* **
424580 ACTCATCCGACGAGGGAGAAGAAGGACATAATGAGAAGAACTTGTTCAACCTTT
65 ACTCATCCGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * *
424634 GTTCGAATCCATCACAAAAGGCGGTGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
1 GTTCGAATCCATCACAGAAGGAGGTAGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
* * *
424699 CTTATTC-AATGAGGGAGAAGAAGTTCATAAT-ATGAAGAACTTGTTCAACCTTA
66 CTCATCCGAA-GAGGGAGAAGAAGTTCATAATGA-GAAGAACTTGTTCAACCTTT
* *
424752 GCTT-GATTCCATCACATAAGGAG
1 G-TTCGAATCCATCACAGAAGGAG
424775 TTGGAACAAC
Statistics
Matches: 415, Mismatches: 69, Indels: 24
0.82 0.14 0.05
Matches are distributed among these distances:
117 7 0.02
118 297 0.72
119 110 0.27
120 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (118 bp):
GTTCGAATCCATCACAGAAGGAGGTAGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
CTCATCCGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
Found at i:424570 original size:237 final size:236
Alignment explanation
Indices: 424161--424767 Score: 692
Period size: 237 Copynumber: 2.6 Consensus size: 236
424151 TCATCACTTC
** * * *
424161 GTTCGAATCCATCACAGGAGGATG-TGGATCAA-AATTTCTAATGGGAGAGTTCATAATGAGAAG
1 GTTCGAATCCATCACAAAAGGA-GATGGATCAACATTTTC-AATGGAAGGGTTCATAATGAGAAG
* * * ** *
424224 AACTCATCCGAAGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTCAAATCC
64 AACTCATCTGAAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTATTTGATTCC
* * * * *
424289 ATCATAGAATAAGGTGTATCAACATTTTCAATGGAAGGGTTCATAATG-AGAAGAACTAAT-TGA
129 ATCACAGAAGAAGGTGTATCAACATTTCCAATGGAAGAGTTCATAATGTA-AAGAACTAATCCG-
* * ***
424352 ATGTGGGAGAAGAAGTTTATAATGAAAAGAACTTGTTCAACCTTT
192 ACGAGGGAGAAGAAGGACATAATGAAAAGAACTTGTTCAACCTTT
* *** *
424397 GTTCGATTCCATCACCGGAGTAGATGGAAT-AACATTTTCAATGGAAGGGTTCATAATGAGAAGA
1 GTTCGAATCCATCACAAAAGGAGATGG-ATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
* * *
424461 ACTCATCTGAAGAGGGAGAAAAACGTTAATAATGAGAAGAACTTGTTTAACCTTTATTTGATTCA
65 ACTCATCTGAAGAGGGAGAAAAA-GTTCATAATGAGAAGAACTTGTTCAACCTTTATTTGATTCC
* * * * *
424526 ATCACAGGAGGAGGTAG-ATCAACATTTCCAATGGGAGAGTTCATAATGTATAGAACTCATCCGA
129 ATCACAGAAGAAGGT-GTATCAACATTTCCAATGGAAGAGTTCATAATGTAAAGAACTAATCCGA
*
424590 CGAGGGAGAAGAAGGACATAATGAGAAGAACTTGTTCAACCTTT
193 CGAGGGAGAAGAAGGACATAATGAAAAGAACTTGTTCAACCTTT
* *
424634 GTTCGAATCCATCACAAAAGGCGGTGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
1 GTTCGAATCCATCACAAAAGGAGATGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
* * * *
424699 CTTAT-TCAATGAGGGAGAAGAAGTTCATAAT-ATGAAGAACTTGTTCAACC-TTAGCTTGATTC
66 CTCATCTGAA-GAGGGAGAAAAAGTTCATAATGA-GAAGAACTTGTTCAACCTTTA-TTTGATTC
424761 CATCACA
128 CATCACA
424768 TAAGGAGTTG
Statistics
Matches: 315, Mismatches: 45, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
235 5 0.02
236 110 0.35
237 197 0.63
238 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (236 bp):
GTTCGAATCCATCACAAAAGGAGATGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
CTCATCTGAAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTATTTGATTCCAT
CACAGAAGAAGGTGTATCAACATTTCCAATGGAAGAGTTCATAATGTAAAGAACTAATCCGACGA
GGGAGAAGAAGGACATAATGAAAAGAACTTGTTCAACCTTT
Found at i:424942 original size:40 final size:40
Alignment explanation
Indices: 424759--424990 Score: 191
Period size: 42 Copynumber: 5.7 Consensus size: 40
424749 TTAGCTTGAT
* *
424759 TCCATCACATAAGGAGTTGGAACAAC-TCTGACCTTGGCACA
1 TCCATCACATAAGGAGTTGGATCAACATC--ACCTTGGCTCA
* * * * *
424800 TCCATCGCATAAGGAGTTGGATCATCATCATCATT-TCTATCG
1 TCCATCACATAAGGAGTTGGATCAACATCA-CCTTGGC--TCA
** * * ** *
424842 TCCATCACATAAGGAGTTTAATCAACATTATCATTTTTCCCA
1 TCCATCACATAAGGAGTTGGATCAACATCA-C-CTTGGCTCA
*
424884 TCCATCACATAAGAAGTTGGATCAACATCACCTTGGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATCACCTTGGCTCA
* *
424924 TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGGTCA
1 TCCATCACATAAGGAGTTGGATCAACATCACCTTGGCTCA
* * * *
424964 ACCATCACA-ACGGAGTAGGGTCAACAT
1 TCCATCACATAAGGAGTTGGATCAACAT
424991 TTCTAAGAGA
Statistics
Matches: 154, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
39 14 0.09
40 52 0.34
41 27 0.18
42 57 0.37
43 2 0.01
44 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (40 bp):
TCCATCACATAAGGAGTTGGATCAACATCACCTTGGCTCA
Found at i:425363 original size:12 final size:12
Alignment explanation
Indices: 425348--425391 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
425338 ACCTGAACTT
425348 AAACCAAGACCC
1 AAACCAAGACCC
425360 AAACCAAGACCC
1 AAACCAAGACCC
* *
425372 AAACCCAGGCCC
1 AAACCAAGACCC
425384 AAAACCAA
1 -AAACCAA
425392 ATCCCTAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.50, C:0.41, G:0.09, T:0.00
Consensus pattern (12 bp):
AAACCAAGACCC
Found at i:429273 original size:18 final size:19
Alignment explanation
Indices: 429228--429273 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
429218 TTTTATCGCA
429228 CTACACACA-ATCCATTTTG
1 CTAC-CACATATCCATTTTG
* *
429247 CCACAACATATCCA-TTTG
1 CTACCACATATCCATTTTG
429265 CTACCACAT
1 CTACCACAT
429274 TGCCATCGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (19 bp):
CTACCACATATCCATTTTG
Found at i:435753 original size:16 final size:16
Alignment explanation
Indices: 435723--435753 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
435713 CAACTTTGTA
*
435723 AAAAAAAAGAGAAAAG
1 AAAAAAAAGAAAAAAG
435739 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
435754 TGAAGCTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:436407 original size:20 final size:20
Alignment explanation
Indices: 436378--436416 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
436368 AGAGCTCATA
*
436378 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
436398 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
436417 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:439978 original size:68 final size:68
Alignment explanation
Indices: 439869--440011 Score: 250
Period size: 68 Copynumber: 2.1 Consensus size: 68
439859 CGTTCATTCA
* *
439869 TCAATCTCAATGCCACATAACTCATCACCTTACCGAGATTCACTCAATGTGTTTAGAGTATAGAA
1 TCAATGTCAATGCCACATAACTCATCACCTTACCGAGATTCACTCAATGTATTTAGAGTATAGAA
439934 AAC
66 AAC
* *
439937 TCAATGTCAATGCCACATAACTCATCACCTTACCGCGATTCACTCAATGTATTTGGAGTATAGAA
1 TCAATGTCAATGCCACATAACTCATCACCTTACCGAGATTCACTCAATGTATTTAGAGTATAGAA
440002 AAC
66 AAC
440005 TCAATGT
1 TCAATGT
440012 TAGAACCAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (68 bp):
TCAATGTCAATGCCACATAACTCATCACCTTACCGAGATTCACTCAATGTATTTAGAGTATAGAA
AAC
Found at i:451241 original size:25 final size:23
Alignment explanation
Indices: 451192--451241 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
451182 AGTTGTTTCA
* *
451192 AATTAATAAATAAAATATTATTT
1 AATTAATAAATAAAATATAAATT
*
451215 AATTAATTCAAATTAAATATAAATT
1 AATTAA-T-AAATAAAATATAAATT
451240 AA
1 AA
451242 AGACTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 15 0.68
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTAATAAATAAAATATAAATT
Found at i:451347 original size:79 final size:77
Alignment explanation
Indices: 451209--451352 Score: 177
Period size: 79 Copynumber: 1.8 Consensus size: 77
451199 AAATAAAATA
*
451209 TTATTTAATTAATTCAAATTAAATATAAATTAAAGACTTATAATCAGAATTATAATA-TTTAATG
1 TTATTTAATTAATTCAAATTAAATATAAATTAAAGACTTATAATCAGAATTACAATATTTTAATG
451273 TTTATTTAAAAC
66 TTTATTTAAAAC
* * * *
451285 TTATTTAATT-ATTCTGAATTATATATATCAATTAAAAGAGTTATAATCTA-AATTACATTATTT
1 TTATTTAATTAATTC-AAATTA-A-ATATAAATT-AAAGACTTATAATC-AGAATTACAATATTT
451348 TAATG
61 TAATG
451353 CTTACTTACT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
75 4 0.07
76 15 0.26
77 1 0.02
78 8 0.14
79 21 0.37
80 8 0.14
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (77 bp):
TTATTTAATTAATTCAAATTAAATATAAATTAAAGACTTATAATCAGAATTACAATATTTTAATG
TTTATTTAAAAC
Found at i:457464 original size:18 final size:18
Alignment explanation
Indices: 457422--457465 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
457412 AAAAATTGGG
*
457422 TGATTTTAATAAAACATT
1 TGATTTTAATAAAACATC
*
457440 TTATTTTAATAAAACA-C
1 TGATTTTAATAAAACATC
457457 TGAGTTTTA
1 TGA-TTTTA
457466 GGGTCTGCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
TGATTTTAATAAAACATC
Found at i:459963 original size:36 final size:36
Alignment explanation
Indices: 459917--460519 Score: 466
Period size: 36 Copynumber: 16.6 Consensus size: 36
459907 GTTTTTAAAA
* * *
459917 AAACCATCTCAAGTGAGATAGATTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * * **
459953 AAACTGTCTCAAGAGAGATAAAATTCATTTCAAGGG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * * * *
459989 AAACGATCT-AA--AAGGT---TTGTGTTTCAAGAG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * **
460019 AAACTGTCTCAAG-GAAGACAAAACTTGTTTCAAGGG
1 AAACTATCTCAAGCG-AGATAAATTTTGTTTCAAGGG
* * * *
460055 AAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGT
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
*
460091 AAACAAAT-TCAA---AG----ATTTTGTTTCAAGGG
1 AAAC-TATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * *
460120 AAAC-AGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 AAACTA-TCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * * * *
460156 AAACTGTCTCAAGAGAGACAAAATTTGTTCCAAGGG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * *
460192 AAA-TCATCTCAAGGGAGAAAAAATTTGTTTCAAGGG
1 AAACT-ATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* * * *
460228 AAACAATCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
* *
460264 AAATTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGAT-AAAT-TT-TGTTTCAAGGG
* * *
460303 AAACTATCTCAAGCAATATAAAATCTTTTGTTTCGAGGG
1 AAACTATCTCAAGCGAGAT-AAA--TTTTGTTTCAAGGG
460342 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGAT-AAA--TTTTGTTTCAAGGG
*
460381 AAACTACCTCAAGCGAGATAAAGTCTTCTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAA-T-TT-TGTTTCAAGGG
* *
460420 AAACTACCTCAAGCGAGATAAAATCTTTTGTTTCAAGTG
1 AAACTATCTCAAGCGAGAT-AAA--TTTTGTTTCAAGGG
* *
460459 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCCAGTG
1 AAACTATCTCAAGCGAGAT-AAAT-TT-TGTTTCAAGGG
460498 AAACTATCTCAAGCGAGATAAA
1 AAACTATCTCAAGCGAGATAAA
460520 ATCTTCTTTA
Statistics
Matches: 476, Mismatches: 60, Indels: 60
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 1 0.00
29 21 0.04
30 16 0.03
31 2 0.00
32 2 0.00
33 7 0.01
35 3 0.01
36 209 0.44
37 7 0.01
38 12 0.03
39 186 0.39
40 7 0.01
41 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
AAACTATCTCAAGCGAGATAAATTTTGTTTCAAGGG
Found at i:460158 original size:101 final size:100
Alignment explanation
Indices: 459940--460314 Score: 439
Period size: 101 Copynumber: 3.6 Consensus size: 100
459930 TGAGATAGAT
** * *
459940 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTCATTTCAAGGGAAACGATCTAAAAGGT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAC-ATCTCAAAGAT
* *
460005 TTGTGTTTCAAGAGAAACTGTCTCAAG-GAAGACAAAA
65 TT-TGTTTCAAGGGAAACAGTCTCAAGAG-AGACAAAA
* *
460042 CTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGTAAACAAAT-TCAAAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAC--ATCTCAAAGA
460106 TTTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA
64 TTTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA
* *
460143 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTCCAAGGGAAATCATCTCAAGGGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAA-CATCTCAA---A
* *
460208 GAAAAAATTTGTTTCAAGGGAAACAATCTCAAGAGAGACAAAA
62 G----ATTTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA
* * * *
460251 TTTGTTTCAAGGGAAATTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA--TT-TGTTTCAAGGGAAAC-ATCTCAA
460315 GCAATATAAA
Statistics
Matches: 237, Mismatches: 21, Indels: 21
0.85 0.08 0.08
Matches are distributed among these distances:
100 2 0.01
101 82 0.35
102 59 0.25
103 2 0.01
104 2 0.01
108 68 0.29
110 3 0.01
111 19 0.08
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (100 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACATCTCAAAGATT
TTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA
Found at i:460305 original size:39 final size:39
Alignment explanation
Indices: 460109--460526 Score: 495
Period size: 39 Copynumber: 11.0 Consensus size: 39
460099 TCAAAGATTT
* *
460109 TGTTTCAAGGGAAAC-AGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTA-TCTCAAGCGAGATAAAATCTTC
* * *
460145 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
460181 TGTTCCAAGGGAAA-TCATCTCAAGGGAGA-AAAA-ATT-
1 TGTTTCAAGGGAAACT-ATCTCAAGCGAGATAAAATCTTC
* * *
460217 TGTTTCAAGGGAAACAATCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
460253 TGTTTCAAGGGAAATTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
460292 TGTTTCGAGGGAAACTATCTCAAGCAATATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
460331 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
460370 TGTTTCAAGGGAAACTACCTCAAGCGAGATAAAGTCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
460409 TGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
*
460448 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
* *
460487 TGTTTCCAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
460526 T
1 T
460527 TTAAAAACAA
Statistics
Matches: 346, Mismatches: 28, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
35 5 0.01
36 117 0.34
37 4 0.01
38 2 0.01
39 218 0.63
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:460627 original size:76 final size:76
Alignment explanation
Indices: 460529--460749 Score: 291
Period size: 76 Copynumber: 2.9 Consensus size: 76
460519 AATCTTCTTT
* *
460529 AAAAACAATCTTGAGTGAAATGAAATTTTTTCTTTCGAGTAAAAACCGTCTCAACCGAGACAAAT
1 AAAAACAATCTTGAGTGAAATGAAATTTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAAAT
460594 CTTGTTTTAAG
66 CTTGTTTTAAG
* * * * * *
460605 AAAAACAATCTTAAGTCAAATGAAATGTCTTCTTTCGAGTAAAAATCGTCTTAAGCGAGAAAAAT
1 AAAAACAATCTTGAGTGAAATGAAATTTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAAAT
* *
460670 CCTGTTTTAAT
66 CTTGTTTTAAG
* * **
460681 AAAAACATTCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACTATCTCAAGCGAGACAGA
1 AAAAACAATCTTGAGTGAAATGAAAT-TTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACA-A
460745 ATCTT
64 ATCTT
460750 CTGTTTCAAG
Statistics
Matches: 122, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
75 4 0.03
76 113 0.93
77 5 0.04
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAATGAAATTTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAAAT
CTTGTTTTAAG
Found at i:460750 original size:41 final size:39
Alignment explanation
Indices: 460702--460798 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 39
460692 TGAGTGAAAT
*
460702 AAATCTTCTTGTTTCGAGTAAAAACTATCT-CAAGCGAGACA
1 AAATCTTC-TGTTTCAAG-AAAAACTATCTCCAA-CGAGACA
* **
460743 GAATCTTCTGTTTCAAGGGAAACTATCTCCAACGAGACA
1 AAATCTTCTGTTTCAAGAAAAACTATCTCCAACGAGACA
*
460782 AAATTTTCTGTTTCAAG
1 AAATCTTCTGTTTCAAG
460799 CGAAATAACT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 31 0.63
40 11 0.22
41 7 0.14
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (39 bp):
AAATCTTCTGTTTCAAGAAAAACTATCTCCAACGAGACA
Found at i:460769 original size:39 final size:39
Alignment explanation
Indices: 460723--460803 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
460713 TTTCGAGTAA
* *
460723 AAACTATCT-CAAGCGAGACAGAATCTTCTGTTTCAAGGG
1 AAACTATCTCCAA-CGAGACAAAATCTTCTGTTTCAAGCG
*
460762 AAACTATCTCCAACGAGACAAAATTTTCTGTTTCAAGCG
1 AAACTATCTCCAACGAGACAAAATCTTCTGTTTCAAGCG
460801 AAA
1 AAA
460804 TAACTCTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (39 bp):
AAACTATCTCCAACGAGACAAAATCTTCTGTTTCAAGCG
Found at i:464941 original size:31 final size:29
Alignment explanation
Indices: 464899--464956 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
464889 CAATAAGAGC
464899 AGACAAAAAGAAATCAATGTTAGTAGAAACA
1 AGACAAAAAG-AATCAA-GTTAGTAGAAACA
* *
464930 AGACAACAAGAATCAAGTTAGTTGAAA
1 AGACAAAAAGAATCAAGTTAGTAGAAA
464957 AGATTAGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (29 bp):
AGACAAAAAGAATCAAGTTAGTAGAAACA
Found at i:474377 original size:21 final size:21
Alignment explanation
Indices: 474353--474393 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
474343 TCAAGATTTG
474353 AAGAGCTTATATTAAAAATCA
1 AAGAGCTTATATTAAAAATCA
*
474374 AAGAGCTTATATTGAAAATC
1 AAGAGCTTATATTAAAAATC
474394 TAATCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
AAGAGCTTATATTAAAAATCA
Found at i:475400 original size:100 final size:100
Alignment explanation
Indices: 475228--475701 Score: 305
Period size: 100 Copynumber: 4.8 Consensus size: 100
475218 CTGATGAGTA
* * * * * *
475228 CATATAGGA-AATCTCATCTACTCTTTCCAGAAGTG-AGGAGAA-TTCATATAGGAGAGGTTTTT
1 CATATAGGAGAAT-TCATATACTCTTTCTAGAAATGCA-AAGAATTTCATATAAGAGAGATTTTT
*
475290 CAACTTCAAAATTGATTTAGTGGGAGAATTAAGAAGT
64 CAACTTCAAAATTGATTTAGTGGGAGAATGAAGAAGT
* * * * *
475327 CATATAGGAGAATTCATATATTCTTTGTAGAAGTGCAAGGAAGTTT-ATATAAGAGAGATTTTTT
1 CATATAGGAGAATTCATATACTCTTTCTAGAAATGCAAAGAA-TTTCATATAAGAGAGATTTTTC
* * *
475391 AACTTCAAAATTGACTTTA-TGGGAGGATGAGGAATT
65 AACTTCAAAATTGA-TTTAGTGGGAGAATGAAGAAGT
* ** * * * *
475427 CATATAGGAGAGTTTGTATACTCTTTCTATAAATGCAAAGAATTTCATATATGGGAGCTTTTTCA
1 CATATAGGAGAATTCATATACTCTTTCTAGAAATGCAAAGAATTTCATATAAGAGAGATTTTTCA
* *
475492 ATTTCAAAATTGATTT-GATTGGAGAATGAAG-AGTT
66 ACTTCAAAATTGATTTAG-TGGGAGAATGAAGAAG-T
* * * * * * * *
475527 CATACAGGAGAGATT-GTGTACTCTTTCCAGAAGT-AAGAAGAAGTTCATAT-AGAAGAGGTTTT
1 CATATAGGAGA-ATTCATATACTCTTTCTAGAAATGCA-AAGAATTTCATATAAG-AGAGATTTT
* * * * *
475589 TCAGCTTCATAATTGACTT-GATGGAAGAAT-AATAAGTT
63 TCAACTTCAAAATTGATTTAG-TGGGAGAATGAAGAAG-T
** * * * * *
475627 CATATAGGAG-ATATCATCCACTCTTTCCA-AAAGTG-AGAATAAGTTCATATATGAGA-AATTT
1 CATATAGGAGAAT-TCATATACTCTTTCTAGAAA-TGCA-AAGAATTTCATATAAGAGAGATTTT
*
475688 TCAGCTTCAAAATT
63 TCAACTTCAAAATT
475702 AACTTGATAA
Statistics
Matches: 299, Mismatches: 58, Indels: 36
0.76 0.15 0.09
Matches are distributed among these distances:
98 2 0.01
99 60 0.20
100 228 0.76
101 9 0.03
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (100 bp):
CATATAGGAGAATTCATATACTCTTTCTAGAAATGCAAAGAATTTCATATAAGAGAGATTTTTCA
ACTTCAAAATTGATTTAGTGGGAGAATGAAGAAGT
Found at i:475605 original size:200 final size:195
Alignment explanation
Indices: 475228--475888 Score: 529
Period size: 199 Copynumber: 3.3 Consensus size: 195
475218 CTGATGAGTA
* * * * *
475228 CATATAGGAAATCTCATCTACTCTTTCCAGAAGTGAGGAGAATTCATATA-GGAGAGGTTTTTCA
1 CATATAGGAGATATCATC-ACTCTTTCCAAAAGTGAGAAGAATTCATATATGG-GAGATTTTTCA
* * *
475292 ACTTCAAAATTGATTT-AGTGGGAGAATTAAGAAG-TCATATAGGAGAATTCATATATTCTTTGT
64 ACTTCAAAATTGATTTGA-TAGGAGAA-TAAG-AGTTCATATAGGAGAATT-GTATATTCTTTCT
* * * * *
475355 AGAAGT-GCAAGGAAGTTTATATA-AGAGAGATTTTTTAACTTCAAAATTGACTTTATGGGAGGA
125 AGAAGTAG-AA-GAAGTTCATATAGA-AGAGATTTTTTAGCTTCATAATTGACTTTATGGAAGAA
475418 TGAGGAATT
187 TGAGGAATT
* * * *
475427 CATATAGGAGAGTTTGTAT-ACTCTTTCTATAAA-TGCA-AAGAATTTCATATATGGGAGCTTTT
1 CATATAGGAGA-TAT-CATCACTCTTTCCA-AAAGTG-AGAAGAA-TTCATATATGGGAGATTTT
* * * * *
475489 TCAATTTCAAAATTGATTTGATTGGAGAATGAAGAGTTCATACAGGAGAGATTGTGTACTCTTTC
61 TCAACTTCAAAATTGATTTGATAGGAGAAT-AAGAGTTCATATAGGAGA-ATTGTATATTCTTTC
* * * *
475554 CAGAAGTAAGAAGAAGTTCATATAGAAGAGGTTTTTCAGCTTCATAATTGACTTGATGGAAGAAT
124 TAGAAGT-AGAAGAAGTTCATATAGAAGAGATTTTTTAGCTTCATAATTGACTTTATGGAAGAAT
**
475619 -AATAAGTT
188 GAGGAA-TT
* * *
475627 CATATAGGAGATATCATCCACTCTTTCCAAAAGTGAGAATAAGTTCATATATGAGA-AATTTTCA
1 CATATAGGAGATATCAT-CACTCTTTCCAAAAGTGAGAAGAA-TTCATATATGGGAGATTTTTCA
* * * ** * * *
475691 GCTTCAAAATTAACTTGATAAAAGACTAAGGAGTTCATATAGGAGAACTTGTCTATTTTTTCTAG
64 ACTTCAAAATTGATTTGATAGGAGAATAA-GAGTTCATATAGGAGAA-TTGTATATTCTTTCTAG
*
475756 AAGTGAGAAGAAGTTCATATATG-AGAGCTTTTTTAGCTTCATAATTGACCTTT-TGGAAGAATG
127 AAGT-AGAAGAAGTTCATATA-GAAGAGATTTTTTAGCTTCATAATTGA-CTTTATGGAAGAATG
**
475819 AGGCGTT
189 AGGAATT
* ** * * * * *
475826 CATATAGGAG-TGCTCATCTTGTCTTGCCCAAATTGAGAAGAAGTTCATATATGAGAGGTTTTT
1 CATATAGGAGAT-ATCATC-ACTCTTTCCAAAAGTGAGAAGAA-TTCATATATGGGAGATTTTT
475889 TTAGCTTTAT
Statistics
Matches: 373, Mismatches: 63, Indels: 51
0.77 0.13 0.10
Matches are distributed among these distances:
198 7 0.02
199 189 0.51
200 165 0.44
201 11 0.03
202 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (195 bp):
CATATAGGAGATATCATCACTCTTTCCAAAAGTGAGAAGAATTCATATATGGGAGATTTTTCAAC
TTCAAAATTGATTTGATAGGAGAATAAGAGTTCATATAGGAGAATTGTATATTCTTTCTAGAAGT
AGAAGAAGTTCATATAGAAGAGATTTTTTAGCTTCATAATTGACTTTATGGAAGAATGAGGAATT
Found at i:475730 original size:99 final size:100
Alignment explanation
Indices: 475228--475882 Score: 285
Period size: 100 Copynumber: 6.6 Consensus size: 100
475218 CTGATGAGTA
* * * **
475228 CATATAGGA-AATCTCATCTACTCTTTCCAGAAGTGAGGAGAA-TTCATATAGGAGAGGTTTTTC
1 CATATAGGAGAA-CTCATCCACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGAATTTTC
* * * ***
475291 AACTTCAAAATTGA-TTTAGTGGGAGAATTAAGAAG-T
65 AGCTTCAAAATTAACTTGA-TAAAAGAA-TAAGAAGTT
* ** * ** * * * * *
475327 CATATAGGAGAATTCATATATTCTTTGTAGAAGTGCA-AGGAAGTTTATATAAGAGAGATTTTTT
1 CATATAGGAGAACTCATCCACTCTTTCCAGAAGTG-AGAAGAAGTTCATATATGAGAGAATTTTC
* * * *** * *
475391 AACTTCAAAATTGACTTTATGGGAGGATGAGGAA-TT
65 AGCTTCAAAATTAACTTGATAAAAGAAT-AAGAAGTT
** ** ** * * * * * **
475427 CATATAGGAGAGTTTGTATACTCTTTCTATAAATGCA-AAGAATTTCATATATGGGAGCTTTTTC
1 CATATAGGAGAACTCATCCACTCTTTCCAGAAGTG-AGAAGAAGTTCATATATGAGAGAATTTTC
** * * ***
475491 AATTTCAAAATTGATTTGATTGGAGAATGAAG-AGTT
65 AGCTTCAAAATTAACTTGATAAAAGAAT-AAGAAGTT
* ** ** * **
475527 CATACAGGAGAGA-TTGTGTACTCTTTCCAGAAGTAAGAAGAAGTTCATATA-GAAGAGGTTTTT
1 CATATAGGAGA-ACTCATCCACTCTTTCCAGAAGTGAGAAGAAGTTCATATATG-AGAGAATTTT
* * ** *
475590 CAGCTTCATAATTGACTTGATGGAAGAATAATAAGTT
64 CAGCTTCAAAATTAACTTGATAAAAGAATAAGAAGTT
* *
475627 CATATAGGAGATA-TCATCCACTCTTTCCAAAAGTGAGAATAAGTTCATATATGAGA-AATTTTC
1 CATATAGGAGA-ACTCATCCACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGAATTTTC
* *
475690 AGCTTCAAAATTAACTTGATAAAAGACTAAGGAGTT
65 AGCTTCAAAATTAACTTGATAAAAGAATAAGAAGTT
** * * * * ** *
475726 CATATAGGAGAACTTGTCTATTTTTTCTAGAAGTGAGAAGAAGTTCATATATGAGAGCTTTTTTA
1 CATATAGGAGAACTCATCCACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGAATTTTCA
* * * ** * **
475791 GCTTCATAATTGACCTT-TTGGAAGAATGAGGCGTT
66 GCTTCAAAATT-AACTTGATAAAAGAATAAGAAGTT
** *** * *
475826 CATATAGGAGTGCTCATCTTGTCTTGCCCA-AATTGAGAAGAAGTTCATATATGAGAG
1 CATATAGGAGAACTCATCCACTCTT-TCCAGAAGTGAGAAGAAGTTCATATATGAGAG
475883 GTTTTTTTAG
Statistics
Matches: 443, Mismatches: 97, Indels: 31
0.78 0.17 0.05
Matches are distributed among these distances:
98 1 0.00
99 116 0.26
100 315 0.71
101 11 0.02
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (100 bp):
CATATAGGAGAACTCATCCACTCTTTCCAGAAGTGAGAAGAAGTTCATATATGAGAGAATTTTCA
GCTTCAAAATTAACTTGATAAAAGAATAAGAAGTT
Found at i:475786 original size:299 final size:299
Alignment explanation
Indices: 475246--475788 Score: 641
Period size: 299 Copynumber: 1.8 Consensus size: 299
475236 AAATCTCATC
* * * *
475246 TACTCTTTCCAGAAGTGAGGAGAATTCATATAGGAGAGGTTTTTCAACTTCAAAATTGATTTAGT
1 TACTCTTTCCAGAAGTAAGAAGAATTCATATAGAAGAGGTTTTTCAACTTCAAAATTGATTGAGT
* * * ** * * *
475311 GGGAGAATTAAGAAGTCATATAGGAGAATTCATATATTCTTTGTAGAAGTGCAAGGAAGTTTATA
66 GGAAGAATTAAGAAGTCATATAGGAGAATTCATACACTCTTTCCAAAAGTGCAAAGAAGTTCATA
* * * * ** * * **
475376 TAAGAGAGATTTTTTAACTTCAAAATTGACTTTATGGGAGGATGAGGAATTCATATAGGAGAGTT
131 TAAGAGAGAATTTTCAACTTCAAAATTAACTTGATGAAAAGATAAGGAATTCATATAGGAGAACT
* * *
475441 TGTATACTCTTTCTATAAATGCAAAGAATTTCATATATGGGAGCTTTTTCAATTTCAAAATTGAT
196 TGTATACTCTTTCTAGAAATGCAAAGAAGTTCATATATGAGAGCTTTTTCAATTTCAAAATTGAT
475506 TTGATTGGAGAATGAAGAGTTCATACAGGAGAGATTGTG
261 TTGATTGGAGAATGAAGAGTTCATACAGGAGAGATTGTG
* *
475545 TACTCTTTCCAGAAGTAAGAAGAAGTTCATATAGAAGAGGTTTTTCAGCTTCATAATTGACTTGA
1 TACTCTTTCCAGAAGTAAGAAGAA-TTCATATAGAAGAGGTTTTTCAACTTCAAAATTGA-TTGA
* * *
475610 -TGGAAGAA-TAATAAGTTCATATAGGAG-ATATCATCCACTCTTTCCAAAAGTG-AGAATAAGT
64 GTGGAAGAATTAAGAAG-TCATATAGGAGAAT-TCATACACTCTTTCCAAAAGTGCA-AAGAAGT
* * *
475671 TCATATATGAGA-AATTTTCAGCTTCAAAATTAACTTGAT-AAAAGACTAAGGAGTTCATATAGG
126 TCATATAAGAGAGAATTTTCAACTTCAAAATTAACTTGATGAAAAGA-TAAGGAATTCATATAGG
* * * *
475734 AGAACTTGTCTATTTTTTCTAGAAGTG-AGAAGAAGTTCATATATGAGAGCTTTTT
190 AGAACTTGTATACTCTTTCTAGAAATGCA-AAGAAGTTCATATATGAGAGCTTTTT
475789 TAGCTTCATA
Statistics
Matches: 200, Mismatches: 37, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
298 4 0.02
299 112 0.56
300 81 0.41
301 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (299 bp):
TACTCTTTCCAGAAGTAAGAAGAATTCATATAGAAGAGGTTTTTCAACTTCAAAATTGATTGAGT
GGAAGAATTAAGAAGTCATATAGGAGAATTCATACACTCTTTCCAAAAGTGCAAAGAAGTTCATA
TAAGAGAGAATTTTCAACTTCAAAATTAACTTGATGAAAAGATAAGGAATTCATATAGGAGAACT
TGTATACTCTTTCTAGAAATGCAAAGAAGTTCATATATGAGAGCTTTTTCAATTTCAAAATTGAT
TTGATTGGAGAATGAAGAGTTCATACAGGAGAGATTGTG
Found at i:481215 original size:20 final size:20
Alignment explanation
Indices: 481169--481217 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
481159 GAATTGAATC
*
481169 AAAACCGAGCAAAATCATGA
1 AAAACCTAGCAAAATCATGA
*
481189 AAAACCTAGCAAAATCTTGA
1 AAAACCTAGCAAAATCATGA
481209 AAAACCTAG
1 AAAACCTAG
481218 TTTTGGAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAACCTAGCAAAATCATGA
Found at i:481718 original size:25 final size:25
Alignment explanation
Indices: 481684--481735 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
481674 GTTCCAAAGT
481684 ATGCCTATGTTAGTAAGATTCTAAC
1 ATGCCTATGTTAGTAAGATTCTAAC
481709 ATGCCTATGTTAGTAAGATTCTAAC
1 ATGCCTATGTTAGTAAGATTCTAAC
481734 AT
1 AT
481736 TTGGTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (25 bp):
ATGCCTATGTTAGTAAGATTCTAAC
Found at i:494574 original size:16 final size:16
Alignment explanation
Indices: 494553--494583 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
494543 CAGTTACATA
*
494553 TCAGGTTTATAATAGG
1 TCAGGTTGATAATAGG
494569 TCAGGTTGATAATAG
1 TCAGGTTGATAATAG
494584 ATCGGGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TCAGGTTGATAATAGG
Found at i:499880 original size:27 final size:27
Alignment explanation
Indices: 499843--499894 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
499833 AAGAGCGGCA
*
499843 GTTGGAACTTCAACGACAGCAGCAGTG
1 GTTGGAACTTCAAAGACAGCAGCAGTG
*
499870 GTTGGAACTTCAAAGATAGCAGCAG
1 GTTGGAACTTCAAAGACAGCAGCAG
499895 CAGCAGCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (27 bp):
GTTGGAACTTCAAAGACAGCAGCAGTG
Found at i:506899 original size:20 final size:20
Alignment explanation
Indices: 506874--506960 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
506864 GTTTTGAATT
*
506874 TCGCAACGCGAATATGGAAA
1 TCGCAACGCGAATATGTAAA
*
506894 TCGCAACGCGAATATGTAAT
1 TCGCAACGCGAATATGTAAA
* *
506914 TCGCAATGCGAATATATAAA
1 TCGCAACGCGAATATGTAAA
* *
506934 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
*
506954 TTGCAAC
1 TCGCAAC
506961 ACAGAAGTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:507496 original size:20 final size:20
Alignment explanation
Indices: 507471--507528 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
507461 TTTAAAACTT
507471 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
507491 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
507511 AAATTCGCAATACGAAAA
1 AAATTCGCAACACGAAAA
507529 CCGCAACACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:507547 original size:20 final size:20
Alignment explanation
Indices: 507475--507555 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
507465 AAACTTAAAT
*
507475 TCGCAACACGAAAATGAAAT
1 TCGCAACACGAAAATGAAAA
*
507495 TCGCAACACGAAAATGAAAT
1 TCGCAACACGAAAATGAAAA
*
507515 TCGCAATAC------GAAAA
1 TCGCAACACGAAAATGAAAA
*
507529 CCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
507549 TCGCAAC
1 TCGCAAC
507556 GCGATTTTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 11 0.22
20 39 0.78
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:507609 original size:20 final size:20
Alignment explanation
Indices: 507559--507609 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
507549 TCGCAACGCG
* *
507559 ATTTTAGTTTCGCGTTGTGA
1 ATTTAAGTTTCGCGTTGCGA
* * *
507579 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
507599 ATTTAAGTTTC
1 ATTTAAGTTTC
507610 AAAAACTACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.51
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:509135 original size:21 final size:21
Alignment explanation
Indices: 509111--509160 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
509101 GTTAGGGGAG
*
509111 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
509132 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
509153 TTACGTGA
1 TTACGTGA
509161 CGACAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:510837 original size:20 final size:20
Alignment explanation
Indices: 510814--510852 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
510804 GATTTTTGAG
* *
510814 TTGCGAATTTGATTTTCGCA
1 TTGCAAATTTGACTTTCGCA
510834 TTGCAAATTTGACTTTCGC
1 TTGCAAATTTGACTTTCGC
510853 GACAATCGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
TTGCAAATTTGACTTTCGCA
Found at i:513591 original size:12 final size:12
Alignment explanation
Indices: 513570--513603 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
513560 GGTTGTGGGT
*
513570 TTTGAGATTGTG
1 TTTGATATTGTG
513582 TTTGATATTGTG
1 TTTGATATTGTG
*
513594 TTTGTTATTG
1 TTTGATATTG
513604 AAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:514215 original size:14 final size:15
Alignment explanation
Indices: 514179--514216 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
514169 GAAATCATTG
514179 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
514194 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
514209 AAAAATTA
1 AAAAATTA
514217 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:514400 original size:20 final size:20
Alignment explanation
Indices: 514373--514453 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
514363 TTTGTTGAGA
*
514373 AATT-AAAATTCGTGTTGCG
1 AATTCAAAAATCGTGTTGCG
*
514392 AATTCAAAAATCGAGTTGCG
1 AATTCAAAAATCGTGTTGCG
** * *
514412 AAAACAAAATTAGTGTTGC-
1 AATTCAAAAATCGTGTTGCG
* *
514431 AATTTAGAAAATCTTGTTGCG
1 AATTCA-AAAATCGTGTTGCG
514452 AA
1 AA
514454 AAGGAAACTT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 7 0.15
20 37 0.80
21 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (20 bp):
AATTCAAAAATCGTGTTGCG
Found at i:514468 original size:20 final size:20
Alignment explanation
Indices: 514445--514493 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
514435 TAGAAAATCT
*
514445 TGTTGCGAAAAGGAAACTTG
1 TGTTGCGAAAAAGAAACTTG
* *
514465 TGTTGTGAAAAAGAAATTTG
1 TGTTGCGAAAAAGAAACTTG
*
514485 CGTTGCGAA
1 TGTTGCGAA
514494 TTTGAAAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAAAAGAAACTTG
Found at i:514469 original size:40 final size:40
Alignment explanation
Indices: 514377--514455 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
514367 TTGAGAAATT
*
514377 AAAATTCGTGTTGCGAATTCAAAAATCGAGTTGCGAAAAC
1 AAAATTAGTGTTGCGAATTCAAAAATCGAGTTGCGAAAAC
* **
514417 AAAATTAGTGTTGC-AATTTAGAAAATCTTGTTGCGAAAA
1 AAAATTAGTGTTGCGAATTCA-AAAATCGAGTTGCGAAAA
514456 GGAAACTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (40 bp):
AAAATTAGTGTTGCGAATTCAAAAATCGAGTTGCGAAAAC
Found at i:514543 original size:21 final size:20
Alignment explanation
Indices: 514484--514553 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
514474 AAAGAAATTT
514484 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
514504 GCGTTACAAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
514524 GCGTTGCGAATTTGGAAAATC
1 GCGTTGCGAATTT-GAAAATC
514545 GCGTTGCGA
1 GCGTTGCGA
514554 GAAAGTAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:514619 original size:20 final size:20
Alignment explanation
Indices: 514580--514620 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
514570 ACGATTGCAA
* *
514580 AAACTGGGTTGCGAATTTGG
1 AAACTGGGTTGCAAAATTGG
*
514600 AAACTGTGTTGCAAAATTGG
1 AAACTGGGTTGCAAAATTGG
514620 A
1 A
514621 GTTCGCGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AAACTGGGTTGCAAAATTGG
Found at i:514645 original size:19 final size:19
Alignment explanation
Indices: 514607--514656 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
514597 TGGAAACTGT
* *
514607 GTTGCAAAATTGGAGTTCGC
1 GTTGC-AAATTTGAGATCGC
514627 GTTGCAAATTTGAGATCGC
1 GTTGCAAATTTGAGATCGC
* *
514646 ATTGCGAATTT
1 GTTGCAAATTT
514657 ATTGGTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (19 bp):
GTTGCAAATTTGAGATCGC
Found at i:518907 original size:21 final size:21
Alignment explanation
Indices: 518883--518927 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
518873 AGTAAAACAA
*
518883 AGTG-AATATTAGATTTAATCG
1 AGTGAAAT-TTAGAATTAATCG
*
518904 AGTGAAATTTTGAATTAATCG
1 AGTGAAATTTAGAATTAATCG
518925 AGT
1 AGT
518928 TTAAGAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (21 bp):
AGTGAAATTTAGAATTAATCG
Found at i:519393 original size:2 final size:2
Alignment explanation
Indices: 519386--519441 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
519376 TCTAATACAT
519386 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519427 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
519442 TAAAAAAGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:525200 original size:3 final size:3
Alignment explanation
Indices: 525192--525302 Score: 78
Period size: 3 Copynumber: 34.7 Consensus size: 3
525182 CAATTTTGCA
* * * * *
525192 TAT TAT TAT TAAT AAA TAT TAAT TGT TAT TAG TAT TAAT TAT TAT GAT
1 TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT
* * *
525240 TAT TAAT TAC TAT TAT TAT TATT TAT TGT TAT TAAT AAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT
*
525288 TGT TCAT TAT TAT TA
1 TAT T-AT TAT TAT TA
525303 AATATTAAGT
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
3 65 0.78
4 18 0.22
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:525257 original size:16 final size:16
Alignment explanation
Indices: 525208--525302 Score: 109
Period size: 16 Copynumber: 5.9 Consensus size: 16
525198 TATTAATAAA
* *
525208 TATTAATTGTTATTAG
1 TATTAATTATTATTAT
*
525224 TATTAATTATTATGAT
1 TATTAATTATTATTAT
*
525240 TATTAATTACTATTAT
1 TATTAATTATTATTAT
* *
525256 TATTATTTATTGTTAT
1 TATTAATTATTATTAT
*
525272 TAATAATTATTATTAT
1 TATTAATTATTATTAT
* *
525288 TGTTCATTATTATTA
1 TATTAATTATTATTA
525303 AATATTAAGT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 65 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (16 bp):
TATTAATTATTATTAT
Found at i:525288 original size:29 final size:29
Alignment explanation
Indices: 525224--525303 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
525214 TTGTTATTAG
* *
525224 TATTAATTATT-ATGATTATTAATTACTAT
1 TATT-ATTATTCATTATTATTAATAACTAT
* * *
525253 TATTATTATTTATTGTTATTAATAATTAT
1 TATTATTATTCATTATTATTAATAACTAT
*
525282 TATTATTGTTCATTATTATTAA
1 TATTATTATTCATTATTATTAA
525304 ATATTAAGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 6 0.14
29 37 0.86
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.59
Consensus pattern (29 bp):
TATTATTATTCATTATTATTAATAACTAT
Found at i:525309 original size:13 final size:13
Alignment explanation
Indices: 525192--525309 Score: 77
Period size: 13 Copynumber: 9.4 Consensus size: 13
525182 CAATTTTGCA
525192 TATTATTATTAAT
1 TATTATTATTAAT
* * *
525205 AAATATTAATT-GT
1 TATTATT-ATTAAT
*
525218 TATTAGTATTAAT
1 TATTATTATTAAT
*
525231 TATTATGATT-AT
1 TATTATTATTAAT
*
525243 TA--ATTACT-AT
1 TATTATTATTAAT
*
525253 TATTATTATTTAT
1 TATTATTATTAAT
* *
525266 TGTTATTAATAAT
1 TATTATTATTAAT
*
525279 TATTATTATT-GT
1 TATTATTATTAAT
*
525291 TCATTATTATTAAA
1 T-ATTATTATTAAT
525305 TATTA
1 TATTA
525310 AGTATATATG
Statistics
Matches: 78, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
10 8 0.10
12 14 0.18
13 52 0.67
14 4 0.05
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (13 bp):
TATTATTATTAAT
Found at i:525976 original size:20 final size:20
Alignment explanation
Indices: 525933--525978 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
525923 AAAAAGGGAA
525933 AAAC-AAAAAAAAAACTTCCG
1 AAACAAAAAAAAAAAC-TCCG
525953 -AACAAAAAGAAAAAAC-CCG
1 AAACAAAAA-AAAAAACTCCG
525972 AAACAAA
1 AAACAAA
525979 TAGGTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.70, C:0.20, G:0.07, T:0.04
Consensus pattern (20 bp):
AAACAAAAAAAAAAACTCCG
Found at i:526421 original size:159 final size:159
Alignment explanation
Indices: 526132--526454 Score: 637
Period size: 159 Copynumber: 2.0 Consensus size: 159
526122 AAGGTTAGGA
526132 GAGGGAAAATGGGGTTTAAGGATCCTTTTTCCACTCCTCAAACCACCGATCTGTGGTATCCGGAG
1 GAGGGAAAATGGGGTTTAAGGATCCTTTTTCCACTCCTCAAACCACCGATCTGTGGTATCCGGAG
526197 AGTCTCAGCGTTTCATCTCCCTTGGTGGGAGAGGAGAAGTTGAGAGAGTTTGGATCTCTTCAAAA
66 AGTCTCAGCGTTTCATCTCCCTTGGTGGGAGAGGAGAAGTTGAGAGAGTTTGGATCTCTTCAAAA
526262 TAAAAAGAAATGTTAAATGAAACAAATGG
131 TAAAAAGAAATGTTAAATGAAACAAATGG
526291 GAGGGAAAATGGGGTTTAAGGATCCTTTTTCCACTCCTCAAACCACCGATCTGTGGTATCCGGAG
1 GAGGGAAAATGGGGTTTAAGGATCCTTTTTCCACTCCTCAAACCACCGATCTGTGGTATCCGGAG
*
526356 AGTCTCAGCGTTTCATCTCCCTTGGTGGGAGAGGAGAAGTTGAGAGAGTTTGGTTCTCTTCAAAA
66 AGTCTCAGCGTTTCATCTCCCTTGGTGGGAGAGGAGAAGTTGAGAGAGTTTGGATCTCTTCAAAA
526421 TAAAAAGAAATGTTAAATGAAACAAATGG
131 TAAAAAGAAATGTTAAATGAAACAAATGG
526450 GAGGG
1 GAGGG
526455 GAATGGCCGG
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 163 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (159 bp):
GAGGGAAAATGGGGTTTAAGGATCCTTTTTCCACTCCTCAAACCACCGATCTGTGGTATCCGGAG
AGTCTCAGCGTTTCATCTCCCTTGGTGGGAGAGGAGAAGTTGAGAGAGTTTGGATCTCTTCAAAA
TAAAAAGAAATGTTAAATGAAACAAATGG
Found at i:526810 original size:76 final size:76
Alignment explanation
Indices: 526675--526823 Score: 255
Period size: 76 Copynumber: 2.0 Consensus size: 76
526665 TTATAGATTA
*
526675 TACCATGTTTGCTCATATTTGAATCTGACCCCACGGTTTACGAATCTTTTGTTTTGGTCACTATT
1 TACCATGTTTGCTCATATTTGAATCTGACCCCAAGGTTTACGAATCTTTTGTTTTGGTCACTATT
526740 TTGTATGAATG
66 TTGTATGAATG
* *
526751 TACCATGTTTGCTCATATTTGAATCTGACCCTAAGGTTTACGAATCTTTT-TTTTGGGTCATTAT
1 TACCATGTTTGCTCATATTTGAATCTGACCCCAAGGTTTACGAATCTTTTGTTTT-GGTCACTAT
526815 TTTGTATGA
65 TTTGTATGA
526824 TTGCCTTTAG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 4 0.06
76 65 0.94
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (76 bp):
TACCATGTTTGCTCATATTTGAATCTGACCCCAAGGTTTACGAATCTTTTGTTTTGGTCACTATT
TTGTATGAATG
Found at i:527538 original size:11 final size:11
Alignment explanation
Indices: 527522--527583 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
527512 ATGATACTAA
527522 TATTTTTATTT
1 TATTTTTATTT
**
527533 TATTTTTATAA
1 TATTTTTATTT
527544 TATTTTTATTTT
1 TATTTTTA-TTT
*
527556 TATTTTT-TAT
1 TATTTTTATTT
527566 TATGTTTTATTT
1 TAT-TTTTATTT
*
527578 AATTTT
1 TATTTT
527584 GGTATTGACG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 5 0.12
11 24 0.59
12 12 0.29
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.76
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:527546 original size:22 final size:21
Alignment explanation
Indices: 527519--527583 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
527509 AAAATGATAC
527519 TAATATTTTTATTTTATTTTT
1 TAATATTTTTATTTTATTTTT
527540 ATAATATTTTTATTTTTATTTTT
1 -TAATATTTTTA-TTTTATTTTT
* *
527563 TATTATGTTTTATTTAATTTT
1 TAATAT-TTTTATTTTATTTT
527584 GGTATTGACG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
22 24 0.62
23 15 0.38
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TAATATTTTTATTTTATTTTT
Found at i:527575 original size:7 final size:6
Alignment explanation
Indices: 527522--527562 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
527512 ATGATACTAA
**
527522 TATTTT TA-TTT TATTTT TA-TAA TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT T
527563 TATTATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:529429 original size:22 final size:22
Alignment explanation
Indices: 529398--529448 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
529388 GACCAGAGTT
*
529398 GATGCTCGATGGAGAGCAAGAA
1 GATGCCCGATGGAGAGCAAGAA
529420 GATGCCCGATGGAGAGCAAGAA
1 GATGCCCGATGGAGAGCAAGAA
529442 GATGCCC
1 GATGCCC
529449 AAAGAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (22 bp):
GATGCCCGATGGAGAGCAAGAA
Found at i:555073 original size:23 final size:23
Alignment explanation
Indices: 555018--555061 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
555008 CGTAAAAGAT
*
555018 CAATCTTTCCTTGAAGGATTGAC
1 CAATCTTTCCTCGAAGGATTGAC
555041 CAATCTTTCCTCGAAGGATTG
1 CAATCTTTCCTCGAAGGATTG
555062 GCCACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (23 bp):
CAATCTTTCCTCGAAGGATTGAC
Found at i:557219 original size:15 final size:15
Alignment explanation
Indices: 557199--557230 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
557189 TGTCTGCTTG
*
557199 TGATGTTTTAAGTTT
1 TGATGTTGTAAGTTT
557214 TGATGTTGTAAGTTT
1 TGATGTTGTAAGTTT
557229 TG
1 TG
557231 TTGCAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (15 bp):
TGATGTTGTAAGTTT
Found at i:559411 original size:2 final size:2
Alignment explanation
Indices: 559404--559442 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
559394 ATGTACTTTA
559404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
559443 AAGATAATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:560908 original size:14 final size:14
Alignment explanation
Indices: 560889--560917 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
560879 ATTCGATTTA
560889 ACTTGAATAACTCG
1 ACTTGAATAACTCG
560903 ACTTGAATAACTCG
1 ACTTGAATAACTCG
560917 A
1 A
560918 AATTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (14 bp):
ACTTGAATAACTCG
Found at i:565114 original size:88 final size:88
Alignment explanation
Indices: 565009--565200 Score: 273
Period size: 88 Copynumber: 2.2 Consensus size: 88
564999 CTAATTTCAT
* * * *
565009 TACTCTTCCATGAAGATCAGA-CTTACAA-TTGGATTATTTCACTACTCTTCCGTGGAGGTTTCA
1 TACTCTTCCGTGGAGATCAGATC-TA-AAGTTGGATTACTTCACTACTCTTCCGTGAAGGTTTCA
565072 TACTTTGCTGAAAAA-TCTGTTCCAC
64 TACTTTGCTGAAAAATTC-GTTCCAC
*
565097 TACTCTTCCGTGGAGATCAGATCTAAAGTTGGATTACTTCACTACTCTTCTGTGAAGGTTTCATA
1 TACTCTTCCGTGGAGATCAGATCTAAAGTTGGATTACTTCACTACTCTTCCGTGAAGGTTTCATA
*
565162 CTTTGCTGAAAAATTCGTTCCAT
66 CTTTGCTGAAAAATTCGTTCCAC
*
565185 TACTCTTCTGTGGAGA
1 TACTCTTCCGTGGAGA
565201 GCGAATTTTG
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
87 2 0.02
88 89 0.95
89 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (88 bp):
TACTCTTCCGTGGAGATCAGATCTAAAGTTGGATTACTTCACTACTCTTCCGTGAAGGTTTCATA
CTTTGCTGAAAAATTCGTTCCAC
Found at i:565425 original size:20 final size:20
Alignment explanation
Indices: 565387--565429 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
565377 AGACTGACAT
565387 ATGACCCAAGGAATTTTACAA
1 ATGACCCAAGG-ATTTTACAA
565408 ATGACCCGAAGG-TTTTACAA
1 ATGACCC-AAGGATTTTACAA
565428 AT
1 AT
565430 TCGTGAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (20 bp):
ATGACCCAAGGATTTTACAA
Found at i:566044 original size:22 final size:22
Alignment explanation
Indices: 566019--566067 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
566009 GATAAAGCTT
566019 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
566041 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
566063 TCATC
1 TCATC
566068 CTTGTAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:566314 original size:24 final size:25
Alignment explanation
Indices: 566264--566314 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
566254 AATCTTAGTT
* *
566264 AGTTCCACTAGTTTCTTATTGTTAA
1 AGTTCCAATAGTTTCTTATTGTGAA
566289 AGTTCCAATA-TTTCTT-TTGTGGAA
1 AGTTCCAATAGTTTCTTATTGT-GAA
566313 AG
1 AG
566315 AAATCTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 10 0.43
25 9 0.39
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (25 bp):
AGTTCCAATAGTTTCTTATTGTGAA
Found at i:572816 original size:16 final size:17
Alignment explanation
Indices: 572784--572817 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
572774 AATGCCTTCA
*
572784 TTTTCTTTATTTCTCTC
1 TTTTCTTTATCTCTCTC
572801 TTTTCTTT-TCTCTCTC
1 TTTTCTTTATCTCTCTC
572817 T
1 T
572818 AGACGAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTTTATCTCTCTC
Found at i:573908 original size:2 final size:2
Alignment explanation
Indices: 573901--573932 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
573891 ATGTTCTCTA
573901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
573933 TAAAAGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577377 original size:43 final size:43
Alignment explanation
Indices: 577300--577419 Score: 197
Period size: 43 Copynumber: 2.8 Consensus size: 43
577290 TAAAACACCT
577300 TAACATACCACCCTTA-CCCCGCACTCCAATATATCATGTCCC
1 TAACATACCACCCTTACCCCCGCACTCCAATATATCATGTCCC
577342 TAACATACCACCCTTACCCCCGCACTCCAATATATCATGTCCC
1 TAACATACCACCCTTACCCCCGCACTCCAATATATCATGTCCC
* * * *
577385 TAACATACCATCCATACCGCCGCACCCCAATATAT
1 TAACATACCACCCTTACCCCCGCACTCCAATATAT
577420 ATCATCATGT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
42 16 0.22
43 57 0.78
ACGTcount: A:0.30, C:0.42, G:0.05, T:0.23
Consensus pattern (43 bp):
TAACATACCACCCTTACCCCCGCACTCCAATATATCATGTCCC
Found at i:577457 original size:48 final size:48
Alignment explanation
Indices: 577328--577521 Score: 193
Period size: 48 Copynumber: 4.1 Consensus size: 48
577318 CCGCACTCCA
* * * *
577328 ATAT-ATCATGTCCCTAACATACCACCCTTACCCCCGCACTCC---A-
1 ATATCATCATGTCCCTAACATACCATCCTTATCGCCGCACACCAATAT
* * *
577371 ATAT-ATCATGTCCCTAACATACCATCCATACCGCCGCACCCCAATAT
1 ATATCATCATGTCCCTAACATACCATCCTTATCGCCGCACACCAATAT
* * * * * *
577418 ATATCATCATGTCCCTAACGTACAATTCTTATCGTCGCACGCCAATAA
1 ATATCATCATGTCCCTAACATACCATCCTTATCGCCGCACACCAATAT
* * *
577466 ATATCATTATGTCCTTAACATACCATCCTTATCGCCGCACACTAATAT
1 ATATCATCATGTCCCTAACATACCATCCTTATCGCCGCACACCAATAT
577514 ATCATCAT
1 AT-ATCAT
577522 ACCATCAGAG
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 38 0.31
46 1 0.01
47 4 0.03
48 76 0.61
49 5 0.04
ACGTcount: A:0.31, C:0.35, G:0.07, T:0.28
Consensus pattern (48 bp):
ATATCATCATGTCCCTAACATACCATCCTTATCGCCGCACACCAATAT
Found at i:580014 original size:66 final size:66
Alignment explanation
Indices: 579898--580025 Score: 172
Period size: 66 Copynumber: 1.9 Consensus size: 66
579888 AGTCTATAAG
* * *
579898 GAATTACCAGTCAGTGATTAACCTATACAATGAATTACCAGCATCGACTGAACTTGCCAGAGATA
1 GAATTACCAGTCAGTGATTAACCTATACAATGAATTACCAGCAGCAACTGAACCTGCCAGAGATA
579963 T
66 T
*
579964 GAATTACCAGTC-GATG-TTGAACCTATACAA-GAAATTACCTGCAGCAACTGAACCTGCCAGAG
1 GAATTACCAGTCAG-TGATT-AACCTATACAATG-AATTACCAGCAGCAACTGAACCTGCCAGAG
580026 TCTTCATACC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
65 4 0.07
66 51 0.93
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (66 bp):
GAATTACCAGTCAGTGATTAACCTATACAATGAATTACCAGCAGCAACTGAACCTGCCAGAGATA
T
Done.